Genes and Proteins


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Mutational and Co-mutational analysis of SARS-CoV-2 Sequences from India revealed different Co-mutation patterns and clade-specific mutations across seven Indian states and one union territory during term2 (April 2020 to July 2020) and term3 (August 2020 to December 2020).
PMID
Title Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India
Author(s) nameNupur Biswas, Priyanka Mallick, Sujay Krishna Maity, Debaleena Bhowmik, Arpita Ghosh Mitra, Soumen Saha, Aviral Roy, Partha Chakrabarti, Sandip Paul, Saikat Chakrabarti
Journal
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Date of publishing2021 Mar 25
Metadata was analyzed to associate the frequent mutations and co-mutation patterns with COVID-19 patient status (deceased, symptomatic, mild, and asymptomatic groups).
PMID
Title Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India
Author(s) nameNupur Biswas, Priyanka Mallick, Sujay Krishna Maity, Debaleena Bhowmik, Arpita Ghosh Mitra, Soumen Saha, Aviral Roy, Partha Chakrabarti, Sandip Paul, Saikat Chakrabarti
Journal
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Date of publishing2021 Mar 25
The study reports a newly identified SARS-CoV-2 Strain from Israel. The strain included a non-synonymous mutation in the S protein: P681H (C23604A) and additional four synonymous mutations, Nsp3:C7765T, Nsp12b: C13821T, Nsp16:T21111C, and C29545A.
PMID
Title A unique SARS-CoV-2 spike protein P681H strain detected in Israel
Author(s) name-
Journal
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Of 3080 SARS-CoV-2 genomes analyzed, ~1.5% genome had a rare missense mutation in three accessory proteins ORF6, ORF7b, and ORF10. The mutation caused several changes in the R-group properties of amino acids.
PMID 33619452
Title Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes
Author(s) nameHassan SS, Choudhury PP, Roy B.
Journal Meta Gene
Impact factor0.88
Citation count1
Date of publishing2021 Jun
Both the clusters (C1, C2) identified in the Amazon basin showed 4 mutations in the ORF1ab region and 1 mutation in the Spike gene but at different positions within the region for each cluster.
PMID 33857136
Title Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin
Author(s) nameBallesteros N, Muñoz M, Patiño LH, Hernández C, González-Casabianca F, Carroll I, Santos-Vega M, Cascante J, Angel A, Feged-Rivadeneira A, Palma-Cuero M, Flórez C, Gomez S, van de Guchte A, Khan Z, Dutta J, Obla A, Alshammary HA, Gonzalez-Reiche AS, Hernandez MM, Sordillo EM, Simon V, van Bakel H, Paniz-Mondolfi AE, Ramírez JD.
Journal PLoS Negl Trop Dis
Impact factor4.4
Citation count
Date of publishing2021 Apr
Mutation analysis of 2213 complete genomes from six geographical regions worldwide revealed 3178 polymorphic sites. Of these polymorphic sites, 58.5% (1861 sites) were non-synonymous, compared with the reference genome, Wuhan-Hu-1. Seven frequent non-synonymous mutations were observed in the global population of SARS-CoV-2.
PMID 33572190
Title Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging
Author(s) nameFlores-Alanis A, Cruz-Rangel A, Rodríguez-Gómez F, González J, Torres-Guerrero CA, Delgado G, Cravioto A, Morales-Espinosa R.
Journal Pathogens
Impact factor3.31
Citation count1
Date of publishing2021 Feb 9
62 mutations identified, including 30 mis-sense mutations, in 22 Moroccan patient isolates showed that Spike_D614G and NSP12_P323L mutations were present in all the analyzed sequences, whereas N_G204R and N_R203K were present in 9 sequences.
PMID 33558859
Title Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco
Author(s) nameBadaoui B, Sadki K, Talbi C, Salah D, Tazi L.
Journal Biosaf Health
Impact factorCant find
Citation count1
Date of publishing2021 Feb 3
SARS-CoV-2 immunosuppressed patients had recurrent deletions in the spike glycoprotein. The deletions altered immunodominant epitope positions within the NTD of S glycoprotein and caused resistance to a neutralizing antibody.
PMID 33536258
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ, Nambulli S, Robinson-McCarthy LR, Bain WG, Haidar G, Duprex WP.
Journal Science
Impact factor20.57
Citation count6
Date of publishing2021 Feb 3
Isolate UF-8 (GenBank accession No. MW221275.1) had 12-nucleotide in-frame deletion within ORF3a that encodes viroporin 3a protein.
PMID 33632859
Title In-Frame 12-Nucleotide Deletion within Open Reading Frame 3a in a SARS-CoV-2 Strain Isolated from a Patient Hospitalized with COVID-19
Author(s) nameLednicky JA, Cherabuddi K, Tagliamonte MS, Elbadry MA, Subramaniam K, Waltzek TB, Morris JG Jr.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2021 Feb 25
Sequence alignment of 22164 SARS-CoV-2 genomes from the GISAID database with the reference genome revealed 9210 single nucleotide changes (C>U being the most abundant), resulting in CpG loss.
PMID 33630074
Title Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction
Author(s) nameSadykov M, Mourier T, Guan Q, Pain A.
Journal J Mol Cell Biol
Impact factor4.4
Citation count1
Date of publishing2021 Feb 25
Mutation analysis of 59MDW SARS-CoV-2 genomes (n=37, collected from JBSA/Lackland military members and beneficiaries from May 14, 2020, to July 28, 2020) revealed 14 non-synonymous mutations in the structural proteins. The effect and the biochemical properties of all mutations were studied.
PMID 33609027
Title Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution
Author(s) nameNazario-Toole AE, Xia H, Gibbons TF.
Journal Mil Med
Impact factor
Citation count1
Date of publishing2021 Feb 20
Mutation analysis of 59MDW SARS-CoV-2 genomes (n=37, collected from JBSA/Lackland military members and beneficiaries from May 14, 2020, to July 28, 2020) revealed 109 nucleotide changes in the coding region of the SARS-CoV-2 genome (which caused 63 unique, non-synonymous amino acid mutations), one mutation in the 5-UTR, and two mutations in the 3UTR.
PMID 33609027
Title Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution
Author(s) nameNazario-Toole AE, Xia H, Gibbons TF.
Journal Mil Med
Impact factor
Citation count1
Date of publishing2021 Feb 20
In this study, Indian SARS-CoV-2 genomes were analyzed to find out genomic variants of SARS-CoV-2 proteins. It was found that ORF1ab, S, N, and ORF3a proteins had higher variants than other SARS-CoV-2 proteins.
PMID 33623833
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A, Choudhury PP, Roy S.
Journal Gene Rep
Impact factor0.61
Citation count1
Date of publishing2021 Feb 19
Mutation analysis of 469 complete Indian SARS-CoV-2 nucleotide sequences from GenBank revealed 536 mutated positions within the coding regions of SARS-CoV-2 proteins.
PMID 33623833
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A, Choudhury PP, Roy S.
Journal Gene Rep
Impact factor0.61
Citation count1
Date of publishing2021 Feb 19
Mutation analysis of 469 complete Indian SARS-CoV-2 nucleotide sequences from GenBank revealed that five proteins ORF1ab, ORF3a, S, N, and M had multiple mutations in different variants. While six proteins ORF6, ORF7a, ORF7b, ORF8, ORF10, and E had a single mutation in each variant.
PMID 33623833
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A, Choudhury PP, Roy S.
Journal Gene Rep
Impact factor0.61
Citation count1
Date of publishing2021 Feb 19
Of 333 non-synonymous mutations (obtained from the Mutation analysis of 469 complete Indian SARS-CoV-2 nucleotide sequences from GenBank), 57 possible deleterious amino acid substitutions are predicted, which may impact the protein stability.
PMID 33623833
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A, Choudhury PP, Roy S.
Journal Gene Rep
Impact factor0.61
Citation count1
Date of publishing2021 Feb 19
Compared to the reference Wuhan Hu-1 genome, the sequenced genome (GenBank accession no. MW079418- MW079427) from Malta/Sliema had 15 nucleotide variations.
PMID 33509993
Title Genome Sequences of 10 SARS-CoV-2 Viral Strains Obtained by Nanopore Sequencing of Nasopharyngeal Swabs in Malta
Author(s) nameBiazzo M, Madeddu S, Elnifro E, Sultana T, Muscat J, Scerri CA, Santoro F, Pinzauti D.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2021 Jan 28
Six mutations were reported in the study, which separates recent ancestors of Group 1 and 2 belonging to B.1.1 lineage from Group 3 belonging to B.1.5 lineage.
PMID 33510171
Title Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia
Author(s) nameKomissarov AB, Safina KR, Garushyants SK, Fadeev AV, Sergeeva MV, Ivanova AA, Danilenko DM, Lioznov D, Shneider OV, Shvyrev N, Spirin V, Glyzin D, Shchur V, Bazykin GA.
Journal Nat Commun
Impact factor11.8
Citation count1
Date of publishing2021 Jan 28
In silico analysis of whole-genome sequences from India revealed the deletions of E protein.
PMID 33166565
Title Deletion in the C-terminal region of the envelope glycoprotein in some of the Indian SARS-CoV-2 genome
Author(s) nameKumar BK, Rohit A, Prithvisagar KS, Rai P, Karunasagar I, Karunasagar I.
Journal Virus Res
Impact factor2.6
Citation count2
Date of publishing2021 Jan 2
The in vitro mutation analysis showed that the D614G mutation changes the spike protein sorting, enhances the trafficking of spike protein to the lysosome, and thus accelerates the entry of SARS-CoV-2 in uninfected cells.
PMID 33330866
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ, Ai Y, Li M, Pekosz A, Cox A, Atai N, Gould SJ.
Journal bioRxiv
Impact factorIts not a journal
Citation count1
Date of publishing2020 Dec 9
Most frequent and prevalent mutation reported, with reference to Wuhan sequence (hCoV-19/Wuhan/WIV04/2019), was P323L in the non-structural protein 12 (94.7%) whereas the second frequent mutation was D614G in the Spike glycoprotein region (92.6%), followed by G71S in the non-structural protein 5 (70%).
PMID 33359061
Title Molecular epidemiology of COVID-19 in Oman: A molecular andsurveillance study for the early transmission of COVID-19 in thecountry
Author(s) nameAl-Mahruqi S, Al-Wahaibi A, Khan AL, Al-Jardani A, Asaf S, Alkindi H, Al-Kharusi S, Al-Rawahi AN, Al-Rawahi A, Al-Salmani M, Al-Shukri I, Al-Busaidi A, Al-Abri SS, Al-Harrasi A.
Journal Int J Infect Dis
Impact factor3.42
Citation count1
Date of publishing2020 Dec 21
Compared to the SARS-CoV-2 reference genome (MN908947.3), the SARS-CoV-2 Isolate USA/AR-UAMS001/2020 (GISAID accession no. EPI_ISL_492181) had seven mutations. And the genome USA/AR-UAMS002/2020 (GISAID accession no. EPI_ISL_492182) had four mutations.
PMID 33334896
Title Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing
Author(s) nameJenjaroenpun P, Wanchai V, Ono-Moore KD, Laudadio J, James LP, Adams SH, Prior F, Nookaew I, Ussery DW, Wongsurawat T.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2020 Dec 17
Compared to the SARS-CoV-2 reference genome (MN908947), the first Tunisian genome (accession number: MT559037) had six nucleotides and four amino acid mutations. And second Tunisian genome (accession number: MT559038) had five nucleotides and two amino acid mutations.
PMID 33034798
Title Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hospital in Tunis
Author(s) nameHandrick S, Bestehorn-Willmann M, Eckstein S, Walter MC, Antwerpen MH, Naija H, Stoecker K, Wölfel R, Ben Moussa M.
Journal Virus Genes
Impact factor
Citation count2
Date of publishing2020 Dec
In the Mutation analysis of Taiwanese SARS-CoV-2 genomes, a 382-nucleotides deletion in the ORF8 gene of the genome Isolate CGMH-CGU-02 (accession number: EPI_ISL_417518) was observed. Three mutations (ORF8-L84S, ORF3a-G251V, and S-D614G) along with one mutation in the ORF1ab gene (V378I) were found frequently within Taiwanese genomes.
PMID 32543353
Title SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East
Author(s) nameGong YN, Tsao KC, Hsiao MJ, Huang CG, Huang PN, Huang PW, Lee KM, Liu YC, Yang SL, Kuo RL, Chen KF, Liu YC, Huang SY, Huang HI, Liu MT, Yang JR, Chiu CH, Yang CT, Chen GW, Shih SR.
Journal Emerg Microbes Infect
Impact factor5.84
Citation count22
Date of publishing2020 Dec
The in-vitro mutation analysis revealed several deleted mutants (Del-muts) and single variants in Vero-E6 cell cultures of a SARS-CoV-2 isolate.
PMID 32301390
Title Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction
Author(s) nameLau SY, Wang P, Mok BW, Zhang AJ, Chu H, Lee AC, Deng S, Chen P, Chan KH, Song W, Chen Z, To KK, Chan JF, Yuen KY, Chen H.
Journal Emerg Microbes Infect
Impact factor5.84
Citation count36
Date of publishing2020 Dec